Stromatolites have been a major focus in the search for ancient microbial biosignatures, in particular, stromatolites containing silicified microfossils. Silicification allows for the preservation of original textures and morphologies, which are important starting criteria in the characterization of fossils’ biogenicity and syngenicity to host rock. The microbial biosignatures of dolomitized stromatolites have not yet been characterized and correlated with their dolomitizing conditions. The Cambrian Allentown Formation in New Jersey is an excellent example of dolomitized stromatolites and thrombolites containing diagenetically modified microbial biosignatures. Based on XRD, ICP-OES, and EPMA data, the dolomite is ordered, and all three generations of dolomite are stoichiometric. The outcrop underwent early dolomitization by meteoric diagenesis and burial diagenesis resulting in multi-generational dolomite formation as follows: (1) The microspar dolomite formed by early replacement of precursory calcium carbonate minerals, at or very near the surface, where mixing of fresh and marine waters produced finely crystalline dolomite, (2) The zoned dolomite formed penecontemporaneously with the microspar phase as rhombohedral crystals by infilling primary pore spaces within the microspar matrix. Cloudy cores observed in many larger dolomite rhombs indicate recrystallization before the crystals grew outward in alternating stages, preserved in zoned rims, of Fe-enriched and -depleted fluids, (3) The saddle dolomite formed during late stage deeper burial with Fe- and Mn-rich fluids and occurs as void-filling, high-temperature phase. Organic carbon, characterized using confocal Raman microscopy, is exclusive to first generation microspar dolomite, and the D and G bands’ characteristics reveal similar style thermal alteration as host rock, indicating that the mapped organic carbon is syngenetic with the Cambrian stromatolites. This study offers a new way to investigate ancient life signatures preserved in secondary dolostones and may aid biosignature detection in ancient carbonate rocks on Mars.